BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124925.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 4,685,944 number of mapped reads = 4,613,763 (98.46%) number of supplementary alignments = 25,065 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,310,362 number of mapped paired reads (second in pair) = 2,303,401 number of mapped paired reads (both in pair) = 4,596,254 number of mapped paired reads (singletons) = 17,509 number of mapped bases = 406,499,259 bp number of sequenced bases = 406,277,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 385,279 duplication rate = 6.02% >>>>>>> Insert size mean insert size = 52,184.3745 std insert size = 2,171,286.0905 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.8725 >>>>>>> ACTG content number of A's = 115,904,694 bp (28.53%) number of C's = 75,238,333 bp (18.52%) number of T's = 122,068,101 bp (30.05%) number of G's = 93,060,525 bp (22.91%) number of N's = 5,744 bp (0%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 2,851,858 number of insertions = 55,441 mapped reads with insertion percentage = 1.17% number of deletions = 132,175 mapped reads with deletion percentage = 2.81% homopolymer indels = 48.93% >>>>>>> Coverage mean coverageData = 0.1313X std coverageData = 1.167X There is a 8.8% of reference with a coverageData >= 1X There is a 2.55% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 37004184 0.14846175247844218 1.4129792239988328 chr2 243199373 33872623 0.139279236546387 1.1839422372954018 chr3 198022430 26009948 0.13134849420845912 0.4855329725247054 chr4 191154276 23289133 0.12183422462388442 0.8700424862527999 chr5 180915260 20589306 0.11380635331701704 0.4571930718439436 chr6 171115067 17222379 0.10064794002038406 0.8999697244850141 chr7 159138663 38283203 0.24056506620267382 2.7514157333685714 chr8 146364022 40357406 0.27573310331687934 0.8258344974414604 chr9 141213431 14521378 0.1028328388961812 1.398932429047717 chr10 135534747 19336215 0.14266610908271368 2.09430324334896 chr11 135006516 19674111 0.14572712179314368 0.8869212881501103 chr12 133851895 22528779 0.16831124430475938 0.5566890842232867 chr13 115169878 8663668 0.07522512092962363 0.3578089652316029 chr14 107349540 10628469 0.09900805350446774 0.47837950900218823 chr15 102531392 8155084 0.07953743571529781 0.37659853468811094 chr16 90354753 8540929 0.09452661555059533 1.109672524369331 chr17 81195210 9646089 0.1188012076081828 1.2202396750904116 chr18 78077248 10513186 0.1346510829889906 1.5634620327054551 chr19 59128983 5050271 0.08541109188365374 0.7749948282272558 chr20 63025520 7170731 0.11377503906354125 0.48129676242274444 chr21 48129895 5083141 0.10561296674343462 0.535419220364543 chr22 51304566 3016483 0.05879560505394393 0.3296234516158952 chrMT 16571 581517 35.09245066682759 20.97773461552724 chrX 155270560 13865289 0.08929760413049324 0.5196393062978213 chrY 59373566 2895737 0.048771485276798095 1.0320422643062392